Publications by authors named "Josefina Lacasa"

2 Publications

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A practical guide to estimating the light extinction coefficient with nonlinear models-a case study on maize.

Plant Methods 2021 Jun 12;17(1):60. Epub 2021 Jun 12.

Department of Agronomy, Kansas State University, 1712 Claflin Rd, Manhattan, KS, 66506, USA.

Background: The fraction of intercepted photosynthetically active radiation (fPARi) is typically described with a non-linear function of leaf area index (LAI) and k, the light extinction coefficient. The parameter k is used to make statistical inference, as an input into crop models, and for phenotyping. It may be estimated using a variety of statistical techniques that differ in assumptions, which ultimately influences the numerical value k and associated uncertainty estimates. A systematic search of peer-reviewed publications for maize (Zea Mays L.) revealed: (i) incompleteness in reported estimation techniques; and (ii) that most studies relied on dated techniques with unrealistic assumptions, such as log-transformed linear models (LogTLM) or normally distributed data. These findings suggest that knowledge of the variety and trade-offs among statistical estimation techniques is lacking, which hinders the use of modern approaches such as Bayesian estimation (BE) and techniques with appropriate assumptions, e.g. assuming beta-distributed data.

Results: The parameter k was estimated for seven maize genotypes with five different methods: least squares estimation (LSE), LogTLM, maximum likelihood estimation (MLE) assuming normal distribution, MLE assuming beta distribution, and BE assuming beta distribution. Methods were compared according to the appropriateness for statistical inference, point estimates' properties, and predictive performance. LogTLM produced the worst predictions for fPARi, whereas both LSE and MLE with normal distribution yielded unrealistic predictions (i.e. fPARi < 0 or > 1) and the greatest coefficients for k. Models with beta-distributed fPARi (either MLE or Bayesian) were recommended to obtain point estimates.

Conclusion: Each estimation technique has underlying assumptions which may yield different estimates of k and change inference, like the magnitude and rankings among genotypes. Thus, for reproducibility, researchers must fully report the statistical model, assumptions, and estimation technique. LogTLMs are most frequently implemented, but should be avoided to estimate k. Modeling fPARi with a beta distribution was an absent practice in the literature but is recommended, applying either MLE or BE. This workflow and technique comparison can be applied to other plant canopy models, such as the vertical distribution of nitrogen, carbohydrates, photosynthesis, etc. Users should select the method balancing benefits and tradeoffs matching the purpose of the study.
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June 2021

Bayesian approach for maize yield response to plant density from both agronomic and economic viewpoints in North America.

Sci Rep 2020 09 29;10(1):15948. Epub 2020 Sep 29.

Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Science Center, Manhattan, KS, 66506, USA.

Targeting the right agronomic optimum plant density (AOPD) for maize (Zea mays L.) is a critical management decision, but even more when the seed cost and grain selling price are accounted for, i.e. economic OPD (EOPD). From the perspective of improving those estimates, past studies have focused on utilizing a Frequentist (classical) approach for obtaining single-point estimates for the yield-density models. Alternative analysis models such as Bayesian computational methods can provide more reliable estimation for AOPD, EOPD and yield at those optimal densities and better quantify the scope of uncertainty and variability that may be in the data. Thus, the aims of this research were to (i) quantify AOPD, EOPD and yield at those plant densities, (ii) obtain and compare clusters of yield-density for different attainable yields and latitudes, and (iii) characterize their influence on EOPD variability under different economic scenarios, i.e. seed cost to corn price ratios. Maize hybrid by seeding rate trials were conducted in 24 US states from 2010 to 2019, in at least one county per state. This study identified common yield-density response curves as well as plant density and yield optimums for 460 site-years. Locations below 40.5 N latitude showed a positive relationship between AOPD and maximum yield, in parallel to the high potential level of productivity. At these latitudes, EOPD depended mostly on the maximum attainable yield. For the northern latitudes, EOPD was not only dependent on the attainable yield but on the cost:price ratio, with high ratios favoring reductions in EOPD at similar yields. A significant contribution from the Bayesian method was realizing that the variability of the estimators for AOPD is sometimes greater than the adjustment accounting for seed cost. Our results point at the differential response across latitudes and commercial relative maturity, as well as the significant uncertainty in the prediction of AOPD, relative to the economic value of the crop and the seed cost adjustments.
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September 2020